Nothing
"plot.sahrlocs" <- function(x, ani=names(x$hr),
var=names(x$sa),
type=c("hr.in.sa", "locs.in.hr", "locs.in.sa"),
ncla=4, ylog = FALSE,
caxis = 0.7, clab = 0.7,
errbar=c("SE", "CI"), alpha=0.05,
draw=TRUE, ...)
{
## Verifications
type<-match.arg(type)
errbar<-match.arg(errbar)
if (!inherits(x, "sahrlocs"))
stop("should be an object of class \"sahrlocs\"")
if (any(is.na(match(ani, names(x$hr)))))
stop(paste("\"",
ani[is.na(match(ani, names(x$hr)))],
"\" is not a valid name"))
if (length(ani)<2)
stop("please select at least 2 individuals")
if (any(is.na(match(var, names(x$sa)))))
stop(paste("\"",
var[is.na(match(var, names(x$sa)))],
"\" is not a valid variable"))
## Graphical settings
ngraph<-length(var)+1
if (draw) {
opar<-par(mfrow=c(1,2), ask=TRUE)
on.exit(par(opar))
}
## Output list
liso<-list()
ty<-strsplit(type, ".in.")[[1]]
## For each habitat variables
for (i in var) {
v<-x$sa[[i]]
## We order the selection ratios if the variable is continuous
if (is.factor(v))
noorder<-TRUE
else
noorder<-FALSE
## Transform the variable into a factor
if (!is.factor(v))
v<-cut(v, breaks=ncla)
## If the available RUs are defined by the study area
if (ty[2]=="sa") {
## the number of units per habitat type
av<-table(v)
nav<-names(av)
av<-as.vector(av)
names(av)<-nav
if (ty[1]=="locs") {
## The used resource units = relocations
locs<-x$locs[ani]
us<-t(as.matrix(as.data.frame(apply(locs,2,
function(x) table(rep(v, x))))))
## The selection ratios
liso[[i]]<-widesII(us, av, alpha=alpha)
## plot them
if (draw)
plot(liso[[i]], ylog=ylog, main=i, clab=clab,
caxis=caxis, errbar=errbar, noorder=noorder)
} else {
## The used resource units = the home range
hr<-x$hr[ani]
hr <- as.data.frame(apply(hr, 2,
function(x) {x[is.na(x)] <- 0; return(x)}))
us<-t(as.matrix(as.data.frame(apply(hr,2,function(x) table(rep(v, x))))))
## The selection ratios
liso[[i]]<-widesII(us, av, alpha=alpha)
## plot them
if (draw)
plot(liso[[i]], ylog=FALSE, main=i,
clab=clab, caxis=caxis, errbar=errbar,
noorder=noorder)
}
} else {
## The home range is available
hr<-x$hr[ani]
hr <- as.data.frame(apply(hr, 2, function(x) {x[is.na(x)] <- 0;
return(x)}))
av<-t(as.matrix(as.data.frame(apply(hr,2,
function(x) table(rep(v, x))))))
locs<-x$locs[ani]
us<-t(as.matrix(as.data.frame(apply(locs,2,
function(x) table(rep(v, x))))))
## Verification that no empty habitat types (not available)
toto<-as.vector(apply(av,2,sum))
av<-av[,toto!=0]
us<-us[,toto!=0]
options(warn=-1)
## selection ratios
liso[[i]]<-widesIII(us, av, alpha=alpha)
options(warn=0)
## plot them
if (draw)
plot(liso[[i]], ylog, main=i, clab=clab,
caxis=caxis, errbar=errbar, noorder=noorder)
}
}
## Output
class(liso)<-"plotsahr"
invisible(liso)
}
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